VMD-L Mailing List

From: Georgios Gerogiokas (G.Gerogiokas_at_sms.ed.ac.uk)
Date: Tue Aug 06 2013 - 10:49:58 CDT

Hi again,

Thanks, for the quick feedback. I suppose it might be easier to just write
a script on the file itself then.

Cheers,
George

Quoting John Stone <johns_at_ks.uiuc.edu> on Tue, 6 Aug 2013 09:51:49 -0500:

>
> Hi,
> As Axel says, there isn't really a way to do this directly, however
> you can export a triangle mesh to one of the file formats in the File|Render
> menu and extract the vertices that way if you like. In order to do that
> an retain the coordinate system of the original molecule, you would also
> need to set the molecule's view/rotate/centering transformation matrices
> to identity before exporting. Let me know if you need more help with that.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
>
> On Tue, Aug 06, 2013 at 01:05:11PM +0200, Axel Kohlmeyer wrote:
>> On Tue, Aug 6, 2013 at 10:44 AM, Georgios Gerogiokas
>> <G.Gerogiokas_at_sms.ed.ac.uk> wrote:
>> > Hi all,
>> >
>> > I was wondering if anyone knows how to extract the
>> > coordinates of the grid points in an isosurface created
>> > at a particular isovalue, for instance from a dx file during
>> > a vmd session.
>>
>> i dont' think this is possible directly, but there are some dusty
>> corners in VMD that i have not looked into for a long time. what might
>> work is to reset view and camera and everything to simple unit
>> transformation and then output the isosurface to a render program and
>> parse the resulting file.
>>
>> axel.
>>
>> >
>> > Many thanks,
>> > George
>> >
>> > --
>> > The University of Edinburgh is a charitable body, registered in
>> > Scotland, with registration number SC005336.
>> >
>> >
>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>> International Centre for Theoretical Physics, Trieste. Italy.
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
>
> 

-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.